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LOC127396574 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9834089-9834615 [ Homo sapiens (human) ]

Gene ID: 127396574, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127396574
Gene description
NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9834089-9834615
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC127396574 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9792405..9792957)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9784359..9784911)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9834089..9834641)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14039 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9773975-9774534 Neighboring gene bromodomain and PHD finger containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19407 Neighboring gene 8-oxoguanine DNA glycosylase Neighboring gene calcium/calmodulin dependent protein kinase I Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14040 Neighboring gene Sharpr-MPRA regulatory region 4794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14041 Neighboring gene transcriptional adaptor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9832484-9832984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14042 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9834616-9835142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19409 Neighboring gene ARPC4-TTLL3 readthrough Neighboring gene actin related protein 2/3 complex subunit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14044 Neighboring gene tubulin tyrosine ligase like 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:9866222-9866442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9867034-9867534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9867535-9868035 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9868869-9869369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9876763-9877262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19411 Neighboring gene RNA pseudouridine synthase D3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 19408
  • ATAC-STARR-seq lymphoblastoid silent region 14043

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_098544.2 

    Range
    101..653
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    9792405..9792957
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    9784359..9784911
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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